Re: [gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes

of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option.* Can you please suggest where might be the problem? Thanks, Sucharita On Wed, Jun 18, 2014 at 7:54 PM, Justin Lemkul wrote: > > > On 6/18/14, 6:47 AM, sucharita dey wrote: > >> Thanks Justin. The OGA

Re: [gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes

)? On Fri, Jun 13, 2014 at 8:41 PM, Justin Lemkul wrote: > > > On 6/13/14, 2:11 AM, sucharita dey wrote: > >> Dear Users, >> >> I have a protein-DNA system with 3 Zinc fingers, 1 Fe++, 1 cofactor NOG >> (N-OxalyGlycine) and crystal waters. >> >> I

Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

n, g_mmpbsa can be compiled using this Gromacs. We will fix this > installation issue in future version. > > ​ > ​ > With Regards, > Rashmi​ > > > > On Mon, Jun 16, 2014 at 11:41 AM, sucharita dey > wrote: > > > Hi Rashmi, > > > > I am facing d

Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

Hi Rashmi, I am facing difficulty in installing the tool you mentioned g_mmpbsa. I am giving this command: ./configure --enable-gmx46 --with-gmx-include=/usr/local/gromacs/include --with-gmx-lib=/usr/local/gromacs/lib configure: error: Could not find /libgmx.a library file I fou

[gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes

Dear Users, I have a protein-DNA system with 3 Zinc fingers, 1 Fe++, 1 cofactor NOG (N-OxalyGlycine) and crystal waters. I have generated the initial topology of OGA from PRODRG and incorporated it in the the forcefield gromos 53a6 and since the forcefield already has parametrs for ZN and FE, I

Re: [gmx-users] asking for N and C termini for DNA and giving error

Thanks Justin. I have very recently started doing MD, guided by Gromacs tutorials; not aware of this issue. Thanks for you suggestion, I will try with Amber ff. Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, National University of Singapore. 14, Medical Drive, #12

Re: [gmx-users] asking for N and C termini for DNA and giving error

rom the current directory while running pdb2gmx. It is not giving error for the modified residue but giving error for DNA terminal. Am I missing anything for which it is not identifying the DNA as "DNA"? -Sucharita Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapo

[gmx-users] asking for N and C termini for DNA and giving error

omacs.org/Documentation/Errors ------- Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, National University of Singapore. 14, Medical Drive, #12-01, Singapore 117599. Tel: (65) 90355220, email: cs...@nus.edu.sg -- Gromacs Users mai

[gmx-users] FW: error after 1ns of md run during production

I have done the subscription, hope my email will be accepted. Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, National University of Singapore. 14, Medical Drive, #12-01, Singapore 117599. Tel: (65) 90355220, email: cs...@nus.edu.sg